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C-terminal domain of adenovirus serotype 5 protein IX assemble into an anti-parallel structure
by single particle (icosahedral) reconstruction, at 22 A resolution
#1: Surface view with section colored by density value, Surface level: -90, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: -90, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1575 |
|---|---|
| Authors | Fabry CMS, Rosa-Calatrava M, Moriscot C, Ruigrok RWH, Boulanger P, Schoehn G |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: -90, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: -90, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Virol., Vol. 83, Issue 2, Page 1135-9, Year 2009 |
|---|---|
| Title | The C-terminal domains of adenovirus serotype 5 protein IX assemble into an antiparallel structure on the facets of the capsid. |
| Authors | Céline M S Fabry, Manuel Rosa-Calatrava, Christine Moriscot, Rob W H Ruigrok, Pierre Boulanger, Guy Schoehn Université Joseph Fourier, Unit for Virus Host Cell Interaction, UMR 5233 UJF-EMBL-CNRS, Grenoble cedex 9, France. |
| Keywords |  Adenoviridae (chemistry), Antibodies, Viral (metabolism), Capsid Proteins (chemistry), Cryoelectron Microscopy, Humans, Models, Molecular, Protein Binding, Protein Structure, Quaternary, hexon capsid protein, Adenovirus |
| Links | DOI: 10.1128/JVI.01808-08, PubMed: 19004948, PMC: PMC2612400 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1575.map ( map file in CCP4 format, 178631 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Integer*2 | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 1135.38 A , B = 1135.38 A , C = 1135.38 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.54 A , Y = 2.54 A , Z = 2.54 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Adenovirus sy12 with anti-sy12 fab | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | SY12 modified adenovirus 5 plus rabbit anti SY12 Fab |
|---|---|
| Number of Components | 1 |
| Details | dodecapeptide TAYSSYMKGGKF (abbreviated SY12 ) fused to the C-terminus of pIX and a recombinant Ad5LacZ-pIX-SY12 vector has been constructed anti SY12 IgG have been clived into FAb using papain and then purified. The complex have been generated using an excess of Fab |
| Component #1: virus - adenovirus 5 | |
| Scientific name | Human adenovirus 5 |
| Common Name | adenovirus 5 |
| Experimental Mass | 150 MDa |
| Details | anti SY12 Fab attached to the C-terminal part of adenovirus 5 protein IX |
| Scientific Name of Species | Human adenovirus 5 (NCBI Taxonomy: 28285) |
| Common Name of Species | adenovirus 5 |
| Empty | No |
| Enveloped | No |
| Isolate | SEROTYPE |
| Class | VIRION |
| Natural Source | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: VERTEBRATES |
| Shell | Diameter: 1000 A T Number: 25 |
 Experiment | |
| Sample Preparation | |
| Staining | Cryo EM |
|---|---|
| Specimen Conc | 1. mg/ml |
| Specimen Support Details | Quantifoil r2/2 |
| Specimen State | particle |
| Buffer | Details: 20mM NaCl, 10mM Tris-HCL pH: 7.5 |
| Vitrification | |
| Method | Blot for 2 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Zeiss |
| Instrument | ZEISS PLUNGE FREEZER CRYOBOX |
| Imaging | |
| Microscope | JEOL 2010F |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 9 e/A**2 |
| Illumination Mode | OTHER |
| Lens | |
| Magnification | Nominal: 30000 X, |
| Astigmatism | Objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 1.4 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 3500 nm |
| Specimen Holder | |
| Holder | Eucentric ( OTHER ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 11 |
| Sampling Size | 7 microns |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | pft |
| Software | pft2 em3dr2 |
| CTF Correction | Each particle |
| Resolution By Author | 22 |
| Resolution Method | FSC at 0.3 cut-off |
| Single Particle | |
| Details | Fab-adenovirus complex |
| Number of Projections | 949 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1575.xml (7.6 KB) | ||
|---|---|---|---|
| Map data | emd_1575.map.gz (56.2 MB) | ||
| Images |  EMD-1575.png (701.3 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1575 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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